Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SIX1

Cell type

Cell type Class
Muscle
Cell type
SMS-CTR
NA
NA

Attributes by original data submitter

Sample

source_name
Fusion Negative Rhabdomyosarcoma
cell type
Fusion Negative Rhabdomyosarcoma
genotype
SIX1 KD
chip antibody
SIX1 (Atlas, HPA0011893)
cell line
SMS-CTR

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. ChIPseq libraries were assembled using the KAPA HyperPrep ChIP library kit following manufacturer's settings and were sequenced on an Illumina Nextseq500 machine.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
26555615
Reads aligned (%)
84.1
Duplicates removed (%)
11.5
Number of peaks
4502 (qval < 1E-05)

hg19

Number of total reads
26555615
Reads aligned (%)
83.6
Duplicates removed (%)
11.6
Number of peaks
4413 (qval < 1E-05)

Base call quality data from DBCLS SRA